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aih-tih-sc-cece97-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-cece97-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 PM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-cece97-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-cece97-R1_A23YTGFLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Jun 03 20:22:13 GMT 2026

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
71510249176	70598893153	5104	63586440081	4599161822	2161393386	251892760	0	0	0	7321124	239737935	1028215	0.029633	0.970367	0	0.900672	0.065145	0.030615	0.003568	0.965817	0.953508	0	0.563922	0.544783	0.709819	0.843147			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.307532
1	0.345505
2	0.399619
3	0.461445
4	0.523389
5	0.582255
6	0.638562
7	0.692152
8	0.744445
9	0.787115
10	0.829822
11	0.872895
12	0.913943
13	0.953839
14	0.995884
15	1.02209
16	1.047027
17	1.064261
18	1.072555
19	1.088143
20	1.10051
21	1.109444
22	1.123687
23	1.133156
24	1.145633
25	1.151417
26	1.154094
27	1.156391
28	1.168186
29	1.167038
30	1.161931
31	1.160862
32	1.156749
33	1.158498
34	1.150889
35	1.155448
36	1.156001
37	1.151431
38	1.159209
39	1.157835
40	1.154358
41	1.160627
42	1.164758
43	1.164437
44	1.158251
45	1.164641
46	1.152824
47	1.146445
48	1.140807
49	1.14076
50	1.139506
51	1.130934
52	1.121135
53	1.124186
54	1.129653
55	1.137022
56	1.140317
57	1.14482
58	1.143601
59	1.141475
60	1.140673
61	1.139438
62	1.133756
63	1.119375
64	1.123755
65	1.119572
66	1.116595
67	1.104534
68	1.106852
69	1.10324
70	1.093271
71	1.079802
72	1.073501
73	1.066118
74	1.061776
75	1.057398
76	1.058327
77	1.052701
78	1.045554
79	1.03436
80	1.020874
81	1.011256
82	0.999819
83	0.985209
84	0.976278
85	0.965356
86	0.949809
87	0.938452
88	0.917424
89	0.896432
90	0.862211
91	0.843488
92	0.81263
93	0.774336
94	0.74047
95	0.711676
96	0.680492
97	0.643086
98	0.60393
99	0.564775
100	0.523625